Skip to main content

Table 1 Retrotransposons that integrate adjacent to tRNA genes

From: Retrotransposon targeting to RNA polymerase III-transcribed genes

Mobile element

Clade

Hosta

Preferred integration site

Host factors mediating this insertion preference

LTR Retrotransposons

Ty1

Ty1-copia

Saccharomyces cerevisiae

~ 1 kb window upstream of RNA Pol III-transcribed genes, including tRNA and 5S rRNA genes [13, 14, 21]

Ty1-IN interaction with Rpc40 [29] and Ty1-IN interaction with Rpc53, Rpc34, Rpc31 [30]

Ty2

Ty1-copia

Saccharomyces cerevisiae

~ 1 kb window upstream of RNA Pol III-transcribed genes [21]

 

Ty3

Ty3-gypsy

Saccharomyces cerevisiae

1–4 bp upstream of tRNA TSSb [93]

Ty3-IN interaction with TFIIIB [88, 89]

Ty3p

Ty3-gypsy

Saccharomyces paradoxus

~ 6 bp upstream of tRNA TSS [110]

 

Ty4

Ty1-copia

Saccharomyces cerevisiae

~ 1 kb window upstream of RNA Pol III-transcribed genes [21]

 

Tj1

Ty3-gypsy

Schizosaccharomyces japonicus

1–10 bp upstream of tRNA TSS [121]

 

Beta/Tca8

Ty3-gypsy

Candida albicans

6-30 bp upstream of tRNA MCSc [119]

 

Tyl3

Ty3-gypsy

Yarrowia lipolytica

~ 5 bp upstream of tRNA TSS [116]

 

Ylt1

Ty3-gypsy

Yarrowia lipolytica

~ 5 bp upstream of tRNA TSS [117]

 

Tyl6

Ty3-gypsy

Yarrowia lipolytica

~ 5 bp upstream of tRNA TSS [115]

 

DGLT-A

Ty3-gypsy

Dictyostelium discoideum

13–33 bp upstream of tRNA MCS [125]

 

Skipper-2

Ty3-gypsy

Dictyostelium discoideum

8–23 bp downstream of tRNA gene [124, 172]

 

Non-LTR Retrotransposons

TRE5

L1

Dictyostelium discoideum

40–54 bp upstream of tRNA MCS; 37–41 bp upstream of extrachromosomal 5S rRNA genes [125, 134, 135, 174]

TRE5 ORF1 interaction with TFIIIB [132]

TRE3

L1

Dictyostelium discoideum

40–150 bp downstream tRNA genes [137, 175]

 

NLTR-A

L1

Dictyostelium purpureum

2–6 bp upstream of tRNA MCS [124]

 

NLTR-B

L1

Polysphondylium pallidum

39–64 bp upstream of tRNA MCS [124]

 
  1. aHost that retrotransposon was first identified in
  2. bTSS refers to the tRNA transcription start site which is ~ 10 bp upstream of the mature tRNA
  3. cMCS refers to the tRNA mature coding sequence